installing apps after completing the jailbreak guide

I haven’t done the jailbreaking procedure yet since I want to gather all the information before starting, so if this is a stupid question, then oops, my bad. I just wanted to make sure that I understand the jail(breaking) process. Am I correct that apps can only be transferred over when the touch is jail-broke and at the end of the tutorial, the touch is back to being jailed so it can sync with itunes? If yes, what steps are required to jailbreak and re-jail the ipod for adding future apps. Lastly, to install apps, do you just use iphuc to copy over the apps, or does it need to be installed and stuff as well? A quick guide for adding apps would be greatly appreciated. Thanks.